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Zinc in PDB 8jws: Ephd Domain of Phd Finger Protein 7 (PHF7)

Protein crystallography data

The structure of Ephd Domain of Phd Finger Protein 7 (PHF7), PDB code: 8jws was solved by I.Bang, H.S.Lee, H.-J.Choi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.01 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.014, 59.145, 170.396, 90, 90, 90
R / Rfree (%) 19.7 / 22.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Ephd Domain of Phd Finger Protein 7 (PHF7) (pdb code 8jws). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Ephd Domain of Phd Finger Protein 7 (PHF7), PDB code: 8jws:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 8jws

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Zinc binding site 1 out of 9 in the Ephd Domain of Phd Finger Protein 7 (PHF7)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ephd Domain of Phd Finger Protein 7 (PHF7) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:13.1
occ:0.97
 ND1 A:HIS58 2.1 9.3 1.0
SG A:CYS36 2.3 13.3 1.0
SG A:CYS61 2.3 12.4 1.0
SG A:CYS33 2.4 11.3 1.0
CE1 A:HIS58 3.0 12.5 1.0
CB A:CYS33 3.0 10.0 1.0
CG A:HIS58 3.1 12.8 1.0
CB A:CYS36 3.2 15.0 1.0
CB A:CYS61 3.3 13.0 1.0
CB A:HIS58 3.4 12.0 1.0
N A:CYS36 3.7 13.5 1.0
CA A:CYS36 4.0 16.7 1.0
N A:HIS58 4.1 8.9 1.0
NE2 A:HIS58 4.1 15.8 1.0
CD2 A:HIS58 4.2 13.1 1.0
CA A:HIS58 4.4 12.5 1.0
CA A:CYS33 4.5 12.0 1.0
CA A:CYS61 4.7 14.4 1.0
C A:LEU35 4.8 16.3 1.0
C A:CYS36 4.8 15.7 1.0
CB A:LEU35 4.9 12.1 1.0
O A:HOH694 4.9 14.0 1.0

Zinc binding site 2 out of 9 in 8jws

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Zinc binding site 2 out of 9 in the Ephd Domain of Phd Finger Protein 7 (PHF7)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ephd Domain of Phd Finger Protein 7 (PHF7) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:15.4
occ:0.95
 ND1 A:HIS120 2.1 15.1 1.0
SG A:CYS101 2.3 17.3 1.0
SG A:CYS123 2.3 16.0 1.0
SG A:CYS98 2.4 13.0 1.0
CE1 A:HIS120 3.0 14.4 1.0
CB A:CYS98 3.1 14.5 1.0
CG A:HIS120 3.2 12.3 1.0
CB A:CYS123 3.2 12.9 1.0
CB A:CYS101 3.4 19.3 1.0
O A:HOH710 3.5 32.2 1.0
CB A:HIS120 3.6 12.9 1.0
N A:CYS101 3.8 18.9 1.0
N A:HIS120 4.1 16.2 1.0
NE2 A:HIS120 4.2 13.5 1.0
CA A:CYS101 4.2 20.6 1.0
CD2 A:HIS120 4.3 13.9 1.0
CA A:HIS120 4.5 12.6 1.0
CA A:CYS98 4.5 15.8 1.0
CB A:VAL100 4.7 16.9 1.0
CA A:CYS123 4.7 19.0 1.0
O A:HOH697 4.8 23.8 1.0
C A:VAL100 4.9 17.2 1.0
C A:CYS101 5.0 22.0 1.0
O A:HIS120 5.0 10.2 1.0

Zinc binding site 3 out of 9 in 8jws

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Zinc binding site 3 out of 9 in the Ephd Domain of Phd Finger Protein 7 (PHF7)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ephd Domain of Phd Finger Protein 7 (PHF7) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:16.8
occ:0.99
 ND1 A:HIS144 2.0 24.8 1.0
SG A:CYS110 2.3 15.5 1.0
SG A:CYS115 2.4 17.0 1.0
SG A:CYS141 2.5 23.6 1.0
CE1 A:HIS144 2.9 27.8 1.0
CG A:HIS144 3.0 23.7 1.0
CB A:CYS115 3.2 23.1 1.0
CB A:CYS110 3.2 12.1 1.0
CB A:CYS141 3.3 23.0 1.0
CB A:HIS144 3.5 20.9 1.0
N A:CYS141 3.9 18.3 1.0
NE2 A:HIS144 4.0 26.3 1.0
CD2 A:HIS144 4.1 27.0 1.0
CA A:CYS141 4.1 16.2 1.0
CG A:LYS143 4.4 44.3 1.0
CB A:ASN112 4.5 17.2 1.0
N A:HIS144 4.6 26.3 1.0
CG A:GLN117 4.6 23.5 1.0
CA A:CYS115 4.6 19.5 1.0
CA A:CYS110 4.7 12.2 1.0
CA A:HIS144 4.7 26.1 1.0
CB A:GLN117 4.7 15.6 1.0
C A:CYS141 4.8 23.4 1.0
O A:CYS141 4.9 23.3 1.0
O A:HOH706 5.0 38.2 1.0
CD A:LYS143 5.0 43.4 1.0

Zinc binding site 4 out of 9 in 8jws

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Zinc binding site 4 out of 9 in the Ephd Domain of Phd Finger Protein 7 (PHF7)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Ephd Domain of Phd Finger Protein 7 (PHF7) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:19.0
occ:1.00
 ND1 B:HIS58 2.1 18.1 1.0
SG B:CYS36 2.3 19.0 1.0
SG B:CYS61 2.3 20.4 1.0
SG B:CYS33 2.4 18.9 1.0
CB B:CYS33 3.1 16.9 1.0
CE1 B:HIS58 3.1 21.6 1.0
CG B:HIS58 3.1 18.8 1.0
CB B:CYS36 3.1 16.6 1.0
CB B:CYS61 3.3 17.9 1.0
CB B:HIS58 3.4 15.5 1.0
N B:CYS36 3.7 20.4 1.0
CA B:CYS36 4.0 23.1 1.0
N B:HIS58 4.2 15.0 1.0
NE2 B:HIS58 4.2 19.7 1.0
CD2 B:HIS58 4.2 19.7 1.0
CA B:HIS58 4.4 14.6 1.0
CA B:CYS33 4.5 22.4 1.0
O B:HOH692 4.7 15.7 1.0
CA B:CYS61 4.7 16.7 1.0
C B:LEU35 4.8 20.8 1.0
C B:CYS36 4.8 26.5 1.0
CB B:LEU35 4.9 20.2 1.0
N B:LEU37 5.0 28.1 1.0

Zinc binding site 5 out of 9 in 8jws

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Zinc binding site 5 out of 9 in the Ephd Domain of Phd Finger Protein 7 (PHF7)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Ephd Domain of Phd Finger Protein 7 (PHF7) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:24.9
occ:1.00
 ND1 B:HIS120 2.2 27.5 1.0
SG B:CYS101 2.3 26.9 1.0
SG B:CYS123 2.3 30.6 1.0
SG B:CYS98 2.3 22.8 1.0
CB B:CYS98 3.1 21.3 1.0
CE1 B:HIS120 3.1 23.5 1.0
CB B:CYS123 3.2 25.9 1.0
CG B:HIS120 3.2 24.5 1.0
CB B:CYS101 3.4 33.3 1.0
CB B:HIS120 3.5 24.4 1.0
N B:CYS101 3.9 28.7 1.0
N B:HIS120 4.1 19.2 1.0
CA B:CYS101 4.2 32.2 1.0
NE2 B:HIS120 4.2 21.4 1.0
CD2 B:HIS120 4.3 20.3 1.0
CA B:HIS120 4.4 18.8 1.0
CA B:CYS98 4.5 25.8 1.0
CA B:CYS123 4.6 29.5 1.0
CB B:VAL100 4.7 30.0 1.0
O B:HIS120 4.9 21.0 1.0
O B:HOH698 5.0 39.8 1.0
C B:CYS101 5.0 34.2 1.0
C B:VAL100 5.0 36.1 1.0

Zinc binding site 6 out of 9 in 8jws

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Zinc binding site 6 out of 9 in the Ephd Domain of Phd Finger Protein 7 (PHF7)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Ephd Domain of Phd Finger Protein 7 (PHF7) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:18.9
occ:0.94
 ND1 B:HIS144 2.1 21.8 1.0
SG B:CYS115 2.3 20.9 1.0
SG B:CYS141 2.3 26.2 1.0
SG B:CYS110 2.3 18.5 1.0
CE1 B:HIS144 3.0 30.9 1.0
CG B:HIS144 3.2 24.0 1.0
CB B:CYS115 3.2 25.2 1.0
CB B:CYS110 3.2 17.3 1.0
CB B:CYS141 3.5 24.6 1.0
CB B:HIS144 3.5 25.8 1.0
N B:CYS141 4.0 21.4 1.0
NE2 B:HIS144 4.2 27.4 1.0
CD2 B:HIS144 4.2 26.5 1.0
CA B:CYS141 4.3 23.0 1.0
CG B:GLN117 4.6 27.4 1.0
CB B:ASN112 4.6 19.8 1.0
CA B:CYS115 4.6 22.6 1.0
CA B:CYS110 4.7 16.1 1.0
CB B:GLN117 4.7 20.9 1.0
N B:HIS144 4.7 30.7 1.0
CG B:LYS143 4.8 47.7 1.0
CA B:HIS144 4.8 30.6 1.0
C B:CYS141 4.8 29.0 1.0
O B:CYS141 4.9 25.8 1.0

Zinc binding site 7 out of 9 in 8jws

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Zinc binding site 7 out of 9 in the Ephd Domain of Phd Finger Protein 7 (PHF7)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Ephd Domain of Phd Finger Protein 7 (PHF7) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:19.3
occ:0.99
 ND1 C:HIS58 2.1 19.2 1.0
SG C:CYS61 2.3 17.9 1.0
SG C:CYS36 2.3 22.2 1.0
SG C:CYS33 2.4 19.4 1.0
CB C:CYS33 3.0 21.7 1.0
CE1 C:HIS58 3.1 17.3 1.0
CG C:HIS58 3.1 15.5 1.0
CB C:CYS36 3.2 19.7 1.0
CB C:CYS61 3.3 13.4 1.0
CB C:HIS58 3.5 14.5 1.0
N C:CYS36 3.7 21.3 1.0
CA C:CYS36 4.0 23.3 1.0
N C:HIS58 4.2 14.7 1.0
NE2 C:HIS58 4.2 19.4 1.0
CD2 C:HIS58 4.2 16.3 1.0
CA C:HIS58 4.4 15.2 1.0
CA C:CYS33 4.5 21.2 1.0
CA C:CYS61 4.7 14.7 1.0
C C:LEU35 4.7 23.5 1.0
C C:CYS36 4.8 31.9 1.0
O C:HOH652 4.8 15.5 1.0
CB C:LEU35 4.8 17.8 1.0
N C:LEU37 5.0 26.7 1.0

Zinc binding site 8 out of 9 in 8jws

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Zinc binding site 8 out of 9 in the Ephd Domain of Phd Finger Protein 7 (PHF7)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Ephd Domain of Phd Finger Protein 7 (PHF7) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:29.8
occ:0.95
 ND1 C:HIS120 2.1 26.9 1.0
SG C:CYS123 2.3 30.7 1.0
SG C:CYS101 2.3 34.0 1.0
SG C:CYS98 2.3 23.7 1.0
CB C:CYS98 3.0 25.6 1.0
CE1 C:HIS120 3.1 28.8 1.0
CG C:HIS120 3.2 19.8 1.0
CB C:CYS123 3.2 29.1 1.0
CB C:CYS101 3.4 34.3 1.0
CB C:HIS120 3.5 22.3 1.0
N C:CYS101 3.8 36.0 1.0
N C:HIS120 4.1 19.9 1.0
CA C:CYS101 4.2 29.7 1.0
NE2 C:HIS120 4.2 26.0 1.0
CD2 C:HIS120 4.3 19.9 1.0
CA C:HIS120 4.4 21.6 1.0
CA C:CYS98 4.5 27.2 1.0
CA C:CYS123 4.7 28.4 1.0
CB C:VAL100 4.7 36.6 1.0
C C:VAL100 4.9 38.0 1.0
C C:CYS101 5.0 36.8 1.0
O C:HIS120 5.0 19.6 1.0

Zinc binding site 9 out of 9 in 8jws

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Zinc binding site 9 out of 9 in the Ephd Domain of Phd Finger Protein 7 (PHF7)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Ephd Domain of Phd Finger Protein 7 (PHF7) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn503

b:19.9
occ:0.95
 ND1 C:HIS144 2.1 27.8 1.0
SG C:CYS141 2.3 22.6 1.0
SG C:CYS115 2.4 22.8 1.0
SG C:CYS110 2.4 22.8 1.0
CE1 C:HIS144 3.1 27.7 1.0
CB C:CYS110 3.1 18.9 1.0
CG C:HIS144 3.2 29.7 1.0
CB C:CYS115 3.2 25.4 1.0
CB C:CYS141 3.4 21.6 1.0
CB C:HIS144 3.5 25.9 1.0
N C:CYS141 4.0 23.0 1.0
NE2 C:HIS144 4.2 28.1 1.0
CA C:CYS141 4.2 20.8 1.0
CD2 C:HIS144 4.3 31.9 1.0
CG C:GLN117 4.5 28.1 1.0
CB C:ASN112 4.6 21.8 1.0
CA C:CYS110 4.6 17.8 1.0
CB C:GLN117 4.6 25.5 1.0
CA C:CYS115 4.7 27.2 1.0
N C:HIS144 4.7 25.3 1.0
CA C:HIS144 4.8 30.7 1.0
C C:CYS141 4.8 20.8 1.0
CG C:LYS143 4.8 45.1 1.0
O C:CYS141 4.9 18.9 1.0

Reference:

H.S.Lee, I.Bang, J.You, T.K.Jeong, C.R.Kim, M.Hwang, J.S.Kim, S.H.Baek, J.J.Song, H.J.Choi. Molecular Basis For PHF7-Mediated Ubiquitination of Histone H3. Genes Dev. 2023.
ISSN: ISSN 0890-9369
PubMed: 37993255
DOI: 10.1101/GAD.350989.123
Page generated: Thu Oct 31 08:28:32 2024

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